This study has focused on the microbial community in a biogas reactor. Microorganisms in the form of bacteria and Archaea are involved in the production of biogas through a process called anaerobic digestion. The microbial community in a biogas reactor is very complex. Recently it has been adopted molecular methods to gain a greater insight. New methods such as "high-throughput" sequencing have made it possible to gain a greater insight into the microbial community. This method can analyze large amounts of data in a relatively short time and at an affordable price. A disadvantage may be relatively short reads of 100 kb, but Illumina MiSeq has temporarily changed this with a reading of 150 kb. The purpose using methods such as FISH, qPCR and sequencing is to identify groups of microorganisms, their role in the biogas process, development of start-up period for biogas reactors with substrate from cattle manure and fish silage, and the occurrence of specific groups of metanogenes in relation to the total incidence of Archaea. The result showed the greatest dominance of bacteria belonging to Firmicutes phylum, while Methanobacteriales demonstrated the greatest dominance among methanogens. In addition to the results obtained, the task has shown that it has been beneficial to combine various methods of analysis of the microbial society. This might be a basis for further work on these methods in related experiments.